corObject-class: Class '"corObject"'

In mariavica/mircomb: An R package for analyzing miRNA-mRNA interactions

Description

Class object for storing all the information for a miRNA-mRNA correlation analysis.

Details

In this version, miRNAs should be preferntially named according to miRBase 17, and mRNAs should be named according to HUGO gene symbol nomenclature.

Objects from the Class

Objects can be created by calls of the form new("corObject", ...).

Slots

dat.miRNA:

Object of class "matrix". Contains the miRNA expression (rows for miRNAs and columns for samples).

dat.mRNA:

Object of class "matrix". Contains the mRNA expression (rows for mRNAs and columns for samples).

pheno.miRNA:

Object of class "data.frame". Rows for samples and columns for phenotypical information.

pheno.mRNA:

Object of class "data.frame". Rows for samples and columns for phenotypical information.

cor:

Object of class "matrix". Rows for miRNAs and columns for mRNAs.

pval:

Object of class "matrix". Rows for miRNAs and columns for mRNAs.

net:

Object of class "data.frame". Rows for unique miRNA:mRNA pairs and columns for their corresponding information (at least: miRNA name, mRNA name, coefficient of correlation and p value).

diffexp.miRNA:

Object of class "data.frame". Rows for miRNAs and columns for their corresponding infomation (usually FC, logratio, mean expression, p value and corrected p value).

diffexp.mRNA:

Object of class "data.frame". Rows for mRNAs and columns for their corresponding infomation (usually FC, logratio, mean expression, p value and corrected p value).

sig.miRNA:

Object of class "vector". Vector specifying the miRNAs that are used for correlation.

sig.mRNA:

Object of class "vector". Vector specifying the mRNAs that are used for correlation.

GO.results:

Object of class "list". It contains the results of a GO analysis.

info:

Object of class "list". It contains the information of the tests and functions used.

Methods

No methods defined with class "corObject" in the signature.

Examples

## minimal corObject:

data(miRNA)
data(mRNA)
data(pheno.miRNA)
data(pheno.mRNA)

minimal<-new("corObject",dat.miRNA=miRNA,dat.mRNA=mRNA,
	pheno.miRNA=pheno.miRNA,pheno.mRNA=pheno.mRNA)

str(minimal)

## corObject with more slots:
data(data.obj)
str(data.obj)

mariavica/mircomb documentation built on Feb. 3, 2020, 2:28 a.m.